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annotator
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Removing the Genomic Annotator and its supporting classes
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2011-07-25 15:10:25 -04:00 |
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beagle
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This commit incorporates several different changes that each pretty much break all the VCF-based integration tests, so I bunched them all together. We now officially emit VCF4.1 files (woo hoo), which means that the VCF headers are now all different (header version is 4.1 plus counts for some of the annotations are 'A' or 'G'). Also, I've added a Read Filter for reads with MQ=255 ('unavailable' in the SAM spec) and have applied this to the UG and the RMS MQ annotation.
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2011-07-12 14:11:53 -04:00 |
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coverage
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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diffengine
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Revert "Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable"
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2011-07-19 18:38:53 -04:00 |
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fasta
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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filters
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This commit incorporates several different changes that each pretty much break all the VCF-based integration tests, so I bunched them all together. We now officially emit VCF4.1 files (woo hoo), which means that the VCF headers are now all different (header version is 4.1 plus counts for some of the annotations are 'A' or 'G'). Also, I've added a Read Filter for reads with MQ=255 ('unavailable' in the SAM spec) and have applied this to the UG and the RMS MQ annotation.
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2011-07-12 14:11:53 -04:00 |
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genotyper
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The Unified Genotyper now does NOT emit SLOD/SB by default; to compute SB use --computeSLOD
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2011-08-02 10:14:21 -04:00 |
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indels
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Don't use the mismatch fraction by default in the RealignerTargetCreator (since it's only useful when using SW in the indel realigner). Also, no more use of -D but instead move over to using VCFs. One integration test is temporarily commented out while I wait for a VCF file to get fixed.
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2011-08-02 10:34:46 -04:00 |
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phasing
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Updated MD5 for PhaseByTransmissionIntegrationTest
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2011-07-26 17:52:25 -04:00 |
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qc
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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recalibration
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Adding MappingQualityUnavailableReadFilter to the SNP and indel CountCovariates
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2011-07-12 15:39:07 -04:00 |
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validation
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When using the BWA bindings, you have to explicitly call close() to get the
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2011-07-21 12:13:29 -04:00 |
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varianteval
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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variantrecalibration
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Walker test system refactoring. All MD5DB related functions are now in MD5DB.java.
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2011-07-18 10:46:01 -04:00 |
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variantutils
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Revert "Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable"
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2011-07-19 18:38:53 -04:00 |
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BAQIntegrationTest.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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ClipReadsWalkersIntegrationTest.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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PileupWalkerIntegrationTest.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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PrintReadsIntegrationTest.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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PrintReadsWalkerUnitTest.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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